Get an initial prototype working! 🎉

cBioPortal · Nov 2, 2024 · c74cad9 · c74cad9
1 parent 7b20055
commit c74cad9
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Showing 6 changed files with 75 additions and 64 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/summary/SummaryApiConfig.java b/src/main/java/org/cbioportal/persistence/summary/SummaryApiConfig.java
@@ -2,7 +2,6 @@
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.stereotype.Component;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -20,44 +19,4 @@ public List<SummaryServer> getServers() {
     public void setServers(List<SummaryServer> servers) {
         this.servers = servers;
     }
-
-    public static class SummaryServer {
-
-        private String name;
-        private String baseUrl;
-        private List<String> studyIds = new ArrayList<>();
-        private List<String> supportedEndpoints = new ArrayList<>();
-
-        public String getName() {
-            return name;
-        }
-
-        public void setName(String name) {
-            this.name = name;
-        }
-
-        public String getBaseUrl() {
-            return baseUrl;
-        }
-
-        public void setBaseUrl(String baseUrl) {
-            this.baseUrl = baseUrl;
-        }
-
-        public List<String> getStudyIds() {
-            return studyIds;
-        }
-
-        public void setStudyIds(List<String> studyIds) {
-            this.studyIds = studyIds;
-        }
-
-        public List<String> getSupportedEndpoints() {
-            return supportedEndpoints;
-        }
-
-        public void setSupportedEndpoints(List<String> supportedEndpoints) {
-            this.supportedEndpoints = supportedEndpoints;
-        }
-    }
 }
diff --git a/src/main/java/org/cbioportal/persistence/summary/SummaryApiImpl.java b/src/main/java/org/cbioportal/persistence/summary/SummaryApiImpl.java
@@ -3,20 +3,20 @@
 import com.fasterxml.jackson.core.JsonFactory;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import org.apache.http.client.utils.URIBuilder;
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataBin;
 import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.web.config.CustomObjectMapper;
 import org.cbioportal.web.parameter.*;
-import org.cbioportal.persistence.summary.SummaryApiConfig.SummaryServer;
 
 import java.net.http.HttpRequest.BodyPublishers;
 import java.net.http.HttpResponse.BodyHandlers;
 
 import java.net.URI;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
+import java.time.Duration;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.CompletableFuture;
@@ -25,12 +25,10 @@ public class SummaryApiImpl implements SummaryApi {
 
     private final SummaryServer summaryServer;
     private final ObjectMapper jsonMapper;
-    private final ObjectMapper yamlMapper;
 
     public SummaryApiImpl(SummaryServer summaryServer) {
         this.summaryServer = summaryServer;
-        jsonMapper = new ObjectMapper(new JsonFactory());
-        yamlMapper = new ObjectMapper(new YAMLFactory());
+        jsonMapper = new CustomObjectMapper();
     }
 
     @Override
@@ -69,7 +67,7 @@ public CompletableFuture<List<ClinicalAttribute>> fetchClinicalAttributes(List<S
     @Override
     public CompletableFuture<List<ClinicalDataCountItem>> fetchClinicalDataCounts(ClinicalDataCountFilter filter) {
         return POST(
-            "/clinical-data-counts",
+            "/clinical-data-counts/fetch",
             Map.of(),
             filter,
             new TypeReference<List<ClinicalDataCountItem>>() {}
@@ -82,7 +80,7 @@ public CompletableFuture<List<ClinicalDataBin>> fetchClinicalDataBinCounts(Clini
             Map.entry("dataBinMethod", dataBinMethod.toString())
         );
         return POST(
-            "/clinical-data-bin-counts",
+            "/clinical-data-bin-counts/fetch",
             params,
             filter,
             new TypeReference<List<ClinicalDataBin>>() {}
@@ -110,18 +108,23 @@ private <T> CompletableFuture<T> POST(
             String payload = jsonMapper.writeValueAsString(data);
 
             // Build the HttpClient/HttpRequest objects
-            HttpClient client = HttpClient.newHttpClient();
+            HttpClient client = HttpClient.newHttpClient(); // TODO dispose after use?
             HttpRequest request = HttpRequest.newBuilder()
                 .uri(uri)
+                .timeout(Duration.ofSeconds(10))
                 .header("Content-Type", "application/json")
                 .POST(BodyPublishers.ofString(payload))
                 .build();
 
             // Send the request asynchronously and try to serialize it into the provided response type
+            System.out.println("POST " + uri);
+            System.out.println("Request body: " + payload);
             return client.sendAsync(request, BodyHandlers.ofString())
                 .thenApply(resp -> {
                     try {
-                        return jsonMapper.readValue(resp.body(), responseType);
+                        String body = resp.body();
+                        System.out.println("Response body: " + body);
+                        return jsonMapper.readValue(body, responseType);
                     } catch (Exception e) {
                         throw new RuntimeException("Could not parse response JSON from " + endpoint, e);
                     }

diff --git a/src/main/java/org/cbioportal/persistence/summary/SummaryServer.java b/src/main/java/org/cbioportal/persistence/summary/SummaryServer.java
@@ -0,0 +1,45 @@
+package org.cbioportal.persistence.summary;
+
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class SummaryServer {
+
+    private String name;
+    private String baseUrl;
+    private List<String> studyIds = new ArrayList<>();
+    private List<String> supportedEndpoints = new ArrayList<>();
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getBaseUrl() {
+        return baseUrl;
+    }
+
+    public void setBaseUrl(String baseUrl) {
+        this.baseUrl = baseUrl;
+    }
+
+    public List<String> getStudyIds() {
+        return studyIds;
+    }
+
+    public void setStudyIds(List<String> studyIds) {
+        this.studyIds = studyIds;
+    }
+
+    public List<String> getSupportedEndpoints() {
+        return supportedEndpoints;
+    }
+
+    public void setSupportedEndpoints(List<String> supportedEndpoints) {
+        this.supportedEndpoints = supportedEndpoints;
+    }
+}
diff --git a/src/main/java/org/cbioportal/web/GenePanelDataController.java b/src/main/java/org/cbioportal/web/GenePanelDataController.java
@@ -30,6 +30,7 @@
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
@@ -82,20 +83,23 @@ public ResponseEntity<List<GenePanelData>> fetchGenePanelDataInMultipleMolecular
         @Valid @RequestAttribute(required = false, value = "interceptedGenePanelDataMultipleStudyFilter") GenePanelDataMultipleStudyFilter interceptedGenePanelDataMultipleStudyFilter,
         @Parameter(required = true, description = "Gene panel data filter object")
         @RequestBody(required = false) GenePanelDataMultipleStudyFilter genePanelDataMultipleStudyFilter) {
-
+        
         List<GenePanelData> genePanelDataList;
         if(CollectionUtils.isEmpty(interceptedGenePanelDataMultipleStudyFilter.getMolecularProfileIds())) {
-            List<MolecularProfileCaseIdentifier> molecularProfileSampleIdentifiers = interceptedGenePanelDataMultipleStudyFilter.getSampleMolecularIdentifiers()
-                .stream()
-                .map(sampleMolecularIdentifier -> {
-                    MolecularProfileCaseIdentifier profileCaseIdentifier = new MolecularProfileCaseIdentifier();
-                    profileCaseIdentifier.setMolecularProfileId(sampleMolecularIdentifier.getMolecularProfileId());
-                    profileCaseIdentifier.setCaseId(sampleMolecularIdentifier.getSampleId());
-                    return profileCaseIdentifier;
-                })
-                .collect(Collectors.toList());
-
-            genePanelDataList = genePanelService.fetchGenePanelDataInMultipleMolecularProfiles(molecularProfileSampleIdentifiers);
+            // Not sure what this does-- stub out for now
+            genePanelDataList = new ArrayList<>();
+
+//            List<MolecularProfileCaseIdentifier> molecularProfileSampleIdentifiers = interceptedGenePanelDataMultipleStudyFilter.getSampleMolecularIdentifiers()
+//                .stream()
+//                .map(sampleMolecularIdentifier -> {
+//                    MolecularProfileCaseIdentifier profileCaseIdentifier = new MolecularProfileCaseIdentifier();
+//                    profileCaseIdentifier.setMolecularProfileId(sampleMolecularIdentifier.getMolecularProfileId());
+//                    profileCaseIdentifier.setCaseId(sampleMolecularIdentifier.getSampleId());
+//                    return profileCaseIdentifier;
+//                })
+//                .collect(Collectors.toList());
+//
+//            genePanelDataList = genePanelService.fetchGenePanelDataInMultipleMolecularProfiles(molecularProfileSampleIdentifiers);
         } else {
             genePanelDataList = genePanelService.fetchGenePanelDataByMolecularProfileIds(new HashSet<>(interceptedGenePanelDataMultipleStudyFilter.getMolecularProfileIds()));
         }

diff --git a/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java b/src/main/java/org/cbioportal/web/parameter/GenePanelDataMultipleStudyFilter.java
@@ -9,7 +9,7 @@ public class GenePanelDataMultipleStudyFilter implements Serializable {
 
     @Size(min = 1, max = PagingConstants.MAX_PAGE_SIZE)
     private List<SampleMolecularIdentifier> sampleMolecularIdentifiers;
-    @Size(min = 1, max = PagingConstants.MAX_PAGE_SIZE)
+    @Size(min = 0, max = PagingConstants.MAX_PAGE_SIZE)
     private List<String> molecularProfileIds;
 
     @AssertTrue

diff --git a/src/main/resources/summary-api.properties b/src/main/resources/summary-api.properties
@@ -1,5 +1,5 @@
 summary.servers[0].name=Enclave Proxy
-summary.servers[0].base-url=http://localhost:8088
+summary.servers[0].base-url=http://host.docker.internal:8088
 summary.servers[0].study-ids[0]=enclave_2024
 summary.servers[0].supported-endpoints[0]=/clinical-attributes/fetch
 summary.servers[0].supported-endpoints[1]=/clinical-data-counts/fetch